Berdych isn't much different from the other big hitters. Federer doesn't like it because he isn't in control. He also doesn't like facing players with big serves, no matter if its the big hitter team (berd, tsonga, delpo, soderling) or the real big servers like Isner.
Fed is also a very tactically gifted player and he benefits playing predicatable players where he can easily read the serve and the groundgame. Berdych is a tricky player to read. Sometimes going ultra-aggressive to the net, sometimes grinding it out from the baseline, sometimes going for broke, sometimes taking pace off. Much better for Roger vs someone like Ferrer where he knows the opponents game exactly and knows what to expect on important points like BPs.
Even if his H2H looks good against most big hitters, he knows if the big hitter catches fire he's done. happened vs delpo in USO, vs Soderling in RG, vs Tsonga in Wimbledon.........vs Berdych next in USO?
I disagree. IMO, it's because Fed has declined in movement and therefore ROS. In his heyday, he had no problems with big servers/hitters (actually he had no problem with anybody consistently except Nadal). He would block their serves and was fast enough to play defensively until they missed. That slight loss of speed translates into not being able to go toe to toe with the youngsters. Instead he's got to use his variety (remember he used to scoff at the drop shot) and more strategy/tactics to stay with them. Plus his confidence is not what it used to be so he's not as free-flowing as he used to be.